# Made by: Beicer C. Tapia
# Plastoquinone (PL9)
# Charges:Gaussian
# 7/26/07
# Updated 2/21/08
# UPDATED 12/12/08 - ADDED AN OXIDIZED REDOX STATE
# Protein: Cytochrome b6f complex
# PDB: 1VF5

# NOTE - THIS FILE DOES NOT CONTAIN THE TAIL OF PLASTOQUINONE
# NOTE - THIS FILE DOES CONTAIN ONLY THE RING OF PLASTOQUINONE
# NOTE - STIGMATELLIN WAS REPLACED BY PLASTOQUINONE (PL1) INSTEAD OF STIGMATELLIN IN THE Qo SITE


CONFLIST PL1        PL1BK PL1DM PL101 PL1-1 

NATOM    PL1BK      0
NATOM    PL1DM      0
NATOM    PL101      21
NATOM    PL1-1      21

IATOM    PL101  C2  0
IATOM    PL101  C3  1
IATOM    PL101  C4  2
IATOM    PL101  C5  3
IATOM    PL101  C6  4
IATOM    PL101  C1  5
IATOM    PL101  C7  6
IATOM    PL101  C52 7
IATOM    PL101  C53 8
IATOM    PL101  O1  9
IATOM    PL101  O2  10
IATOM    PL101 1H52 11
IATOM    PL101 2H52 12
IATOM    PL101 3H52 13
IATOM    PL101 1H53 14
IATOM    PL101 2H53 15
IATOM    PL101 3H53 16
IATOM    PL101  HC2 17
IATOM    PL101 1HC7 18
IATOM    PL101 2HC7 19
IATOM    PL101 3HC7 20
IATOM    PL1-1  C2  0
IATOM    PL1-1  C3  1
IATOM    PL1-1  C4  2
IATOM    PL1-1  C5  3
IATOM    PL1-1  C6  4
IATOM    PL1-1  C1  5
IATOM    PL1-1  C7  6
IATOM    PL1-1  C52 7
IATOM    PL1-1  C53 8
IATOM    PL1-1  O1  9
IATOM    PL1-1  O2  10
IATOM    PL1-1 1H52 11
IATOM    PL1-1 2H52 12
IATOM    PL1-1 3H52 13
IATOM    PL1-1 1H53 14
IATOM    PL1-1 2H53 15
IATOM    PL1-1 3H53 16
IATOM    PL1-1  HC2 17
IATOM    PL1-1 1HC7 18
IATOM    PL1-1 2HC7 19
IATOM    PL1-1 3HC7 20

ATOMNAME PL101    0  C2 
ATOMNAME PL101    1  C3 
ATOMNAME PL101    2  C4 
ATOMNAME PL101    3  C5 
ATOMNAME PL101    4  C6 
ATOMNAME PL101    5  C1 
ATOMNAME PL101    6  C7 
ATOMNAME PL101    7  C52
ATOMNAME PL101    8  C53
ATOMNAME PL101    9  O1 
ATOMNAME PL101   10  O2 
ATOMNAME PL101   11 1H52
ATOMNAME PL101   12 2H52
ATOMNAME PL101   13 3H52
ATOMNAME PL101   14 1H53
ATOMNAME PL101   15 2H53
ATOMNAME PL101   16 3H53
ATOMNAME PL101   17  HC2
ATOMNAME PL101   18 1HC7
ATOMNAME PL101   19 2HC7
ATOMNAME PL101   20 3HC7
ATOMNAME PL1-1    0  C2 
ATOMNAME PL1-1    1  C3 
ATOMNAME PL1-1    2  C4 
ATOMNAME PL1-1    3  C5 
ATOMNAME PL1-1    4  C6 
ATOMNAME PL1-1    5  C1 
ATOMNAME PL1-1    6  C7 
ATOMNAME PL1-1    7  C52
ATOMNAME PL1-1    8  C53
ATOMNAME PL1-1    9  O1 
ATOMNAME PL1-1   10  O2 
ATOMNAME PL1-1   11 1H52
ATOMNAME PL1-1   12 2H52
ATOMNAME PL1-1   13 3H52
ATOMNAME PL1-1   14 1H53
ATOMNAME PL1-1   15 2H53
ATOMNAME PL1-1   16 3H53
ATOMNAME PL1-1   17  HC2
ATOMNAME PL1-1   18 1HC7
ATOMNAME PL1-1   19 2HC7
ATOMNAME PL1-1   20 3HC7

#1.Basic Conformer Information: name, pka, em, rxn.
#23456789A123456789B123456789C
PROTON   PL101      0   
PKA      PL101      0.0 
ELECTRON PL101      0   
EM       PL101      0.0 
RXN      PL101     -2.43

#1.Basic Conformer Information: name, pka, em, rxn.
#23456789A123456789B123456789C
PROTON   PL1-1      0   
PKA      PL1-1      0.0 
ELECTRON PL1-1      0   
EM       PL1-1      0.0 
RXN      PL1-1     -13.08 

#2.Structure Connectivity
#23456789A123456789B123456789C123456789D123456789E123456789F123456789G123456789H123456789I
#ONNECT   conf atom  orbital  ires conn ires conn ires conn ires conn ires conn
#ONNECT |-----|----|---------|----|----|----|----|----|----|----|----|----|----|
CONNECT  PL101  C2        sp2    0  C3     0  C1     0  HC2 
CONNECT  PL101  C3        sp2    0  C2     0  C4     0  C7  
CONNECT  PL101  C4        sp2    0  C3     0  C5     0  O1  
CONNECT  PL101  C5        sp2    0  C4     0  C6     0  C52 
CONNECT  PL101  C6        sp2    0  C5     0  C1     0  C53 
CONNECT  PL101  C1        sp2    0  C2     0  C6     0  O2  
CONNECT  PL101  C7        sp3    0  C3     0 1HC7    0 2HC7    0 3HC7
CONNECT  PL101  C52       sp3    0  C5     0 1H52    0 2H52    0 3H52 
CONNECT  PL101  C53       sp3    0  C6     0 1H53    0 2H53    0 3H53 
CONNECT  PL101  O1          s    0  C4  
CONNECT  PL101  O2          s    0  C1  
CONNECT  PL101 1H52         s    0  C52 
CONNECT  PL101 2H52         s    0  C52 
CONNECT  PL101 3H52         s    0  C52 
CONNECT  PL101 1H53         s    0  C53 
CONNECT  PL101 2H53         s    0  C53 
CONNECT  PL101 3H53         s    0  C53 
CONNECT  PL101  HC2         s    0  C2  
CONNECT  PL101 1HC7         s    0  C7  
CONNECT  PL101 2HC7         s    0  C7  
CONNECT  PL101 3HC7         s    0  C7

#ONNECT   conf atom  orbital  ires conn ires conn ires conn ires conn ires conn
#ONNECT |-----|----|---------|----|----|----|----|----|----|----|----|----|----|
CONNECT  PL1-1  C2        sp2    0  C3     0  C1     0  HC2 
CONNECT  PL1-1  C3        sp2    0  C2     0  C4     0  C7  
CONNECT  PL1-1  C4        sp2    0  C3     0  C5     0  O1  
CONNECT  PL1-1  C5        sp2    0  C4     0  C6     0  C52 
CONNECT  PL1-1  C6        sp2    0  C5     0  C1     0  C53 
CONNECT  PL1-1  C1        sp2    0  C2     0  C6     0  O2  
CONNECT  PL1-1  C7        sp3    0  C3     0 1HC7    0 2HC7    0 3HC7
CONNECT  PL1-1  C52       sp3    0  C5     0 1H52    0 2H52    0 3H52 
CONNECT  PL1-1  C53       sp3    0  C6     0 1H53    0 2H53    0 3H53 
CONNECT  PL1-1  O1          s    0  C4  
CONNECT  PL1-1  O2          s    0  C1  
CONNECT  PL1-1 1H52         s    0  C52 
CONNECT  PL1-1 2H52         s    0  C52 
CONNECT  PL1-1 3H52         s    0  C52 
CONNECT  PL1-1 1H53         s    0  C53 
CONNECT  PL1-1 2H53         s    0  C53 
CONNECT  PL1-1 3H53         s    0  C53 
CONNECT  PL1-1  HC2         s    0  C2  
CONNECT  PL1-1 1HC7         s    0  C7  
CONNECT  PL1-1 2HC7         s    0  C7  
CONNECT  PL1-1 3HC7         s    0  C7

#3.Atom Parameters: Partial Charges and Radii
# from parseres.siz
RADIUS   PL101  C2  1.70
RADIUS   PL101  C3  1.70
RADIUS   PL101  C4  1.70
RADIUS   PL101  C5  1.70
RADIUS   PL101  C6  1.70
RADIUS   PL101  C1  1.70
RADIUS   PL101  C7  1.70
RADIUS   PL101  C52 1.70
RADIUS   PL101  C53 1.70
RADIUS   PL101  O1  1.40
RADIUS   PL101  O2  1.40
RADIUS   PL101 1H52 1.00
RADIUS   PL101 2H52 1.00
RADIUS   PL101 3H52 1.00
RADIUS   PL101 1H53 1.00
RADIUS   PL101 2H53 1.00
RADIUS   PL101 3H53 1.00
RADIUS   PL101  HC2 1.00
RADIUS   PL101 1HC7 1.00
RADIUS   PL101 2HC7 1.00
RADIUS   PL101 3HC7 1.00

CHARGE   PL101  C2  -0.38
CHARGE   PL101  C3   0.00
CHARGE   PL101  C4   0.51
CHARGE   PL101  C5  -0.12
CHARGE   PL101  C6  -0.14
CHARGE   PL101  C1   0.63
CHARGE   PL101  C7  -0.03
CHARGE   PL101  C52  0.04
CHARGE   PL101  C53  0.04
CHARGE   PL101  O1  -0.46
CHARGE   PL101  O2  -0.50
CHARGE   PL101 1H52  0.02
CHARGE   PL101 2H52  0.02
CHARGE   PL101 3H52  0.02
CHARGE   PL101 1H53  0.027
CHARGE   PL101 2H53  0.027
CHARGE   PL101 3H53  0.027
CHARGE   PL101  HC2  0.17
CHARGE   PL101 1HC7  0.033
CHARGE   PL101 2HC7  0.033
CHARGE   PL101 3HC7  0.033

CHARGE   PL1-1  C2  -0.46
CHARGE   PL1-1  C3   0.00
CHARGE   PL1-1  C4   0.36
CHARGE   PL1-1  C5  -0.14
CHARGE   PL1-1  C6  -0.17
CHARGE   PL1-1  C1   0.57
CHARGE   PL1-1  C7   0.11
CHARGE   PL1-1  C52  0.16
CHARGE   PL1-1  C53  0.09
CHARGE   PL1-1  O1  -0.63
CHARGE   PL1-1  O2  -0.70
CHARGE   PL1-1 1H52 -0.04
CHARGE   PL1-1 2H52 -0.04
CHARGE   PL1-1 3H52 -0.05
CHARGE   PL1-1 1H53 -0.03
CHARGE   PL1-1 2H53 -0.03
CHARGE   PL1-1 3H53 -0.01
CHARGE   PL1-1  HC2  0.13
CHARGE   PL1-1 1HC7 -0.04
CHARGE   PL1-1 2HC7 -0.04
CHARGE   PL1-1 3HC7 -0.04

TORSION  PL101 1HC7  C7   C3   C2   f        0.0         3      0.00
TORSION  PL101 1H52  C52  C5   C4   f        0.0         3      0.00
TORSION  PL101 1H53  C53  C6   C5   f        0.0         3      0.00

TORSION  PL1-1 1HC7  C7   C3   C2   f        0.0         3      0.00
TORSION  PL1-1 1H52  C52  C5   C4   f        0.0         3      0.00
TORSION  PL1-1 1H53  C53  C6   C5   f        0.0         3      0.00

